Recently I saw something pretty cool. It’s a motion capture device, but it doesn’t use cameras. As you might’ve already guessed, it uses some well-placed (and talkative) silicon instead. Imagine a suit you put on that will record your every movement in three dimensions, via 17 sensors and a wireless data feed.

This has some pretty cool features. Whereas the traditional motion capture systems we are familiar with require things like a nice camera setup, a well-lit space, and a suit covered in little balls, the Motionwerx suit just needs your movement, and a computer. Further, if you think about it there are some obvious places motion capture as-we-know-it has a very hard time indeed, such as picking up movements that are hidden by the mover’s body position, or by a partner, when more than one person is moving together. And underwater, for example? I haven’t seen anything yet that can do that. Until now, that is.

Okay, so that’s all very great. But here’s a thought about a potential killer app from the oh-my-god-this-could-change-everything department. What about the field of motion emulation, which is to say, learning to do things that require movement, like play sports? Or learning to dance? Imagine for a moment, once a motion capture is acquired, you could put on a Motionwerx suit, and receive rapid feedback as you attempt to emulate the movements you want to learn. Want to swing a golf club exactly like tiger woods? Learn the Rumba? Swim like Michael Phelps? Grapple like Marcelo Garcia? Now, theoretically, you could, and with a minimum of overhead.

I imagine it would look something like this: A model of the motion profile captured from the athlete whose movement is to be emulated is loaded into the learning console.

As you move with the suit on, you receive feedback indicating how closely you match the target, perhaps via tiny vibration packs near each of the sensors, as well as an audible tone that rates an assignable metric, and a visual color coded display which can be observed in real time and reviewed after each attempt. The feedback system is optimized to coach you to improve incrementally with each attempt, setting a new, achievable goal each time, helping you home in closer to target each time. And because the sensors are in so many distinct locations, it is possible to work on different aspects sequentially, e.g. legs, then arms, then head, and then focusing on left elbow, right elbow, etc…

Naturally, you may not be physically identical to the person from whom your target motion is captured. Therefore there are some interesting calibrations to be done to  your own baseline profile, determined by your size and range of movement. It could actually be quite fascinating to experience firsthand in your own body the best match to the movements of several different successful athletes and interpret how these different styles of movement feel in your body and then develop your own, perhaps changeable, modes of performance. Babe Ruth, for example, had a highly unconventional, yet highly successful style of hitting a baseball–rocked back on his heels, and with an endomorphic body type to boot–which would be possible to mimic in your own body and then contrast with the hitting style of Jose Canseco or BarryBonds, again, in your own body.

I find myself thinking about Long John Silver. A lot. Was his crutch better than mine? Did he ever manage to carry a cup of grog more than three feet without throwing it all over the walls? Could this character really have existed and gotten so much done while hopping around on one foot? Arrrrrrr!

I have been avoiding beer all these weeks, because I want to avoid its diuretic effects and extra ambulation that entails. And there’s another thing. I don’t particularly like them shaken all to hell, which is your only choice if a beverage is going to ride in your hand or the drink holder on your crutches while you attempt to drag your carcass from a to b. But last night I decided to indulge in a bottle of nice beer (oboy oboy oboy, my preciousss). I put it in a bag and carried the bag on my back to get down the stairs and to the other room where I would bivouac (you can’t just go somewhere when you’re on crutches. every movement requires planning and provisions and a projected length of stay). Nonetheless, before I could open it and begin to enjoy my little prize, the bottle somehow ended up falling out of the bag, banging on the floor, and rolling away from me across the room, while I just leaned on my crutches like a helpless idiot, watching it go. I could see it turning to foam inside the bottle as it rolled away. ‘Yup, there it goes,’ I thought.

Bottom line: Sippy cups, Euro crutches, Iceman, Exercise. And a spouse/significant other who is bound to you by vows, law, guilt, blackmail, or binding magic of some kind, preferably who has a good sense of personal cost-benefit-analysis. Or, y’know, love and stuff.

If I could do it all over again: I’d buy an Airdyne exercise bike (the kind where you pull with your hands in addition to pedaling), and ideally, some kind of motorized tricycle, quad, or golf cart that can be controlled entirely by hands and left foot, and won’t fall over. ‘Cause the surgery was on my right foot, and the inability to get around at all on your own is exasperating.

Anaesthesia: I elected to have a spinal, with no sedative. It’s not that bad. You roll on your side, they give you a little local anesthetic shot in your back, and then administer the spinal anesthetic and you lie back down. then your lower back and butt starts to feel a little funny, in my case it felt good, like all the tension was running out of my lower body and it was sort of glowing. or something. Anyway, then there’s a motorized tourniquet around your leg somewhere that you can’t feel anyway. In my case I could just see the video screen the surgeon was using to see inside my ankle. So I could watch the entirety of the arthroscopic procedure, which was great. There is a cloth screen across your waist, and the anesthesiologist sits next to you and keeps you company. With the various monitors attached to me I had something else to watch, and made a game of trying to get my heart rate down (46 bpm was my best). I’m not going to pretend it wasn’t disturbing, because it was. I mean it’s surgery. Somebody is cutting on you and that shouldn’t feel right or hunky dory. But after a little while I got into it and watched the little video screen and focused on how cool it was that this awful nagging injury was getting fixed right before my eyes, and I got to see exactly how. It is a small miracle really. It is something you could simply never possibly do yourself, and here it is happening, being executed with the utmost skill and modern techniques, a team of people fixing your parts, while you wait so to speak. To me this is preferable to having some vague period of lost time where something was done to me which I may never fully understand and waking up confused and feeling like I got hit by a truck. They said the spinal could take six hours to wear off, sitting in the recovery room. It didn’t. It took all of 45 minutes or so, the hardest part being convincing the staff that I was ready to crutch on out of there. And they gave me a private little room to recover in because of the spinal too, in case it took a long time, so I wouldn’t have to be in the fray of the recovery room. I watched as the general anesthesia victims were wheeled in one after another, confused, disoriented people who had to be spoken to like idiot children, gently encouraged to return and accept the reality the rest of us could plainly see. No thank you.

I had my computer, my music, things to read, and an urgency to get on my merry way home. So yes, while it was a little gory and disconcerting in there, I say go for it, two thumbs up. Perhaps the most disturbing thing will be how nonchalant the whole thing is for your surgical team. At times I wanted to tell the chatty cathy nurse to quit yammering on in my surgeon’s ear about nonsensical tripe so he could do his job. But the steady progress I was witnessing on the screen told me he is an expert at tuning her out. Or at least that’s what I hoped. I forgot to mention how the second surgery went, the ligament shortening. This is not arthroscopic. It’s good old fashioned, cut-a-big-hole-so-you-can-reach-your-big-human-hands-in-there kinda surgery. I could make out a little of what was going on via a shiny metal mount on the ceiling that the light was attached to. Basically it just looked like a lot of gloved hands crammed in a circle on my ankle, looking a bit like animals on a kill perhaps. Even if I’d had a nice mirror, I wouldn’t have been able to see much. So that part was a little boring. All I could do was chat with the anesthesiologist and ask him questions about the surgery and what was happening here and there. Then pretty soon there suturing it up and you’re almost out of the OR. The OR, by the way, was a fairly large room, with me in the middle, lots of light, and equipment all over the place. Honestly it felt a bit like being in some kind of equipment room or large maintenance closet. Sort of a utility room with tools and stuff here and there around the periphery. Mostly open space. When you’re done, they team up and lift you over onto the wheelie cart-bed and out you go. You’re done!

I’d be remiss, I suppose, if I didn’t mention the most disturbing part of the microfracture procedure. The actual microfracture is a process of making holes in the bone surface of your joint. I was imagining a drill on the end of fancy micro-robot arm or something. It was a bit more medieval than that, a hammer and chisel (punch), to be specific. So there is some hammering. And it does shake your body. But hey, focus on the healing, right? It may feel like a baby sledge, but it’s really just the rhythmic love taps of Asclepius’ own staff, tappity-tapping into your bone to release the youthful fountain of stem cells and blood so you can be a fleet-footed Hermes once again. Once the careful, loving–and undistracted–hands of your skilled and confident surgeon have made enough holes (nobody kept count, but it was quite a few, a bit like those lines of holes woodpeckers make in trees, but don’t think about woodpeckers), they will loosen the tourniquet a bit and watch the screen to see that the blood comes out those holes like it’s sposed to, which was the only blood I saw the whole day, and it was on a vid screen. So there you go. I say ‘most disturbing’, but that’s not to assume it is very disturbing. It’s an odd sensation, to be sure. But whether it’s disturbing, I leave up to you, the patient, to decide for yourself. And remember, your buddy the anesthesiologist, is there to help you out anytime you need it. Drugs? He’s got drugs. In my case, the oddest thing was that it was in those creepiest, uh, oddest moments I mean, that my heart rate dipped the lowest. Weird. A reverse stress response perhaps? Surgery can be whole new experience, an interesting event in your life. Memorable. And if it’s not going that way for you when it’s going down, just say ‘hey, new buddy, hit me’, and it can all be gone, off to la-la land for you hermes. See ya in recovery.

Oh, also. I forgot to mention. No need for catheters in your stuff, at least with the spinal. One thing they do say about the spinal though. You may never pee again. Okay not really. But the first time after the spinal is a triumph you shall tell your grandkids about. And one that few men have had, so there’s that.

Another odd sensory portion of the ligament surgery was a brief whiff of burning flesh due to the cauterizing scalpel. No big deal.

It’s been 5 weeks now since surgery. I am more accustomed now to being crippled but still not liking it. Every day starts with the pain in my hands when I stand with the crutches and take my first steps. About those crutches: After the surgery I had both the usual American crutches, that go up to your armpits, and European crutches, that go up to your forearms. I immediately selected the Euro crutches. They are short and tactical. I can easily get into the car and hold them across my lap, ready to get out of the car again, crutches in front of me. I can climb stairs four at a time. Let me tell you, this is a big deal. Down stairs I can do even more. It is like having huge long front limbs that you can still bend at the elbow. It’s a bit like being one of those big strider beasts in The Dark Crystal. If you haven’t seen that movie, you really should.

With the shortie Euro crutches, I am constantly working my arms and shoulders, which is good. When I climb stairs four at a time, at least I feel like I’m accomplishing something, there is a challenge beyond the tedium of being really slow and lousy at getting around. The tradeoff is that all the weight goes into your hands. Again and again and again. And again. I have gone through about 5 different versions of improvised grip designs now. The stock grips they came with were beautifully sculpted and cushioned, but the angle was wrong. They tweaked my wrists at almost a right angle, putting a ton of stress on them. From Judo (and pretty much every martial art) I have learned that a straight wrist is strong. The stock grips were also left and right specific, rather than ambidextrous, which turned out to be a real pain when you have to put down and pick up your crutches a thousand times a day. Having to sort out right and left every damn time is an extra pain in the ass added to an already annoying practice. In the end, I managed to take the foamie grips off my American crutches and cram them onto the Euro crutch handles, after carving down some plastic ridges that were in the way on the Euro crutches. To this I added a little rubber pad at the base of the grip made from bicycle inner tube pieces. This puts the ulnar side of my palm (opposite the thumb side) on a higher pad and evens out the pressure across the base of my palm, keeping the hand straight. To this I eventually added a pair of long, thick ski socks, pulled over the grip and doubled back a few times to create a big cushy wad of padding to grab onto. I take these on and off periodically to vary how I’m using my hands. I don’t want my hands always curled into the same shape like little gnarled claws. Frequently changing the grip size helps with this a bit.

My personal best on stairs is 5 steps at once going up, and 7 steps going down, not including the starting step. These are the little games that help keep you going.

And then there is the most important crutch mod: a goddamn drink holder. Guess what? when you are crutches you can’t carry things! I took a bicycle water bottle cage and attached it to the back of the crutch with some short, fat, self-tapping screws. You must have this. It is essential equipment. In addition, my lovely spouse/driver took me to the neighborhood REI store where I bought a selection of grown-up sippy cups. A super thermos mug for coffee and such, another mug with carabiner clip handle (ended up not being so useful, but still like it and use it), a drink bottle with sucker-nipple thing, and lastly, a rather cute little insulated cup for grown-up drinky-drinks. Ha!

For the microfracture, all you get is this little love bite. The left one’s for the camera, the right one, just visible, is for the tools. 1 week post surgery.

If you get the Brostrom, this little beauty can be yours.
Hey, maybe I should just add to it and make a happy face.

This is the most important thing in the whole blog. A bike bottle cage attached to the crutch with a couple of coarse thread screws

Proteins

Prion-Like Model:

1. protein folding variants are possible, stable

2. protein folding variants affect and effect protein function

3. protein folding variants are transmissible and retainable

3a. can catalyze each other and stabilize each other

3b. can be dominant, recessive, etc…

3c. are heritable

4. protein folding variants are malleable, variable

If the above is possible, then, it is possible for molecules other than DNA such as proteins to contain heritable and mutable functional traits

Therefore, DNA sequence variation is not necessary for heritable phenotypic change

We can apply this logic to other molecules (carbs, etc…) of course as well.

This model appears to me far more fertile ground for adaptive evolution and essentially everything for which the DNA molecule has become, with increasing suspiciousness, to be apparently insufficient.

Lamarck will get his day.

April 23, 2010 

Central dogma of protein folding: primary sequence determines tertiary structure.

Chaperone proteins counter this dogma by affecting and effecting folding states of other proteins.

Further, prions counter it by effecting folded states of their own (like) protein sequences, even (already) folded ones

Viral proteins have been (especially early on) favorites for structure/folding studies.  These form a biased (easy) set because they essentially must be able to determine tertiary structure from primary sequence, having no cytoplasm of their own and thus rely on host cells for all of the folding environment.  However  this does not mean they are unaffected by differences in that cellular environment among hosts.  Perhaps this is quite the contrary, and could account for some very interesting differences in host choice and pathogenicity, etc…

Historically, energetic calculations show many, many folding variants are possible, and that there are small differences in energy among them, and even the unfolded state.  In test cases, expos, some sequences were used to ‘successfully’ predict tertiary structures, which were ‘confirmed’ by x-ray crystallography.  But x-ray itself is only one (or more) folding choice under certain conditions, often folded free of cellular milieu, and itself still allows some freedom of the actual structures that can produce a given x-ray diffraction pattern.

So my question is, and the answer to this within the scientific community is almost always ‘yes’: have we continually selected for hypotheses, experimental subjects, analytical methods, and conclusions which significantly over-simplify the biological phenomenon taking place.  As in the past, this should be signified by a gradually ever increasing divergence between observation and dogma–a nagging knot in the stomach that something is off, unaccounted for.

As an analogy, imagine fora moment that DNA is indeed the dogmatic ‘blueprint’ of life, of the cell.  It is at least a parts list, that much is clear.  Now the rest of the cell is full of the artisans, the carpenters, their building methods, tools, and even the physical workshop in which construction occurs.  The nature of all of these things has a dramatic effect on the finished product that may be produced.  Further, when we see a completed structure such as a house, we might assume that it came from and be a replicate of written plans specifying its form and construction down to the minutest detail.  In fact however, these plans could be anything as simple as a parts and materials list and the simple phrase “build a house”.  Even from a precise (particular, non-coded) blueprint, a skilled work crew will then follow certain building practices to make the component parts and produce the finished house.  The work crew itself is a great repository of construction information.  The biological analogy would be a construction crew building a house and living it, insularly, and then spawning more buildings and work crews imitating the prior ones.  Even if the written information is fairly well conserved, the workers and their unwritten information, is adaptable, mutable, and heritable.  They can adapt and respond to changes in material availability (nutrition), and changes in weather of other environmental pressures (selective forces).  But the information content of the plans goes hand in hand with the information content of the builders.  And it works best in this way.  If the structures were built by computerized machines following the exact specifications of hard coded, written information, even if some intelligence and adaptability is encoded into it, will be fundamentally limited without the ability to edit its own code.

April 23rd, 2010

‘Cellular culture’

Hypothesis: just as DNA is like a written record, the broader cellular milieu of biomolecules is like a culture within that cell.  This culture forms the all-important mutable and self-replicating context in which the written record of DNA is interpreted and acted upon.

Molecules like chaperones and prions are thus very interesting characters as potential players in this culture.  In cell lineage and sexual reproduction the cellular culture is always passed on; just as DNA is conserved and passed on (and mutable), so is cellular context.

I would expect that as the complexity of the organism increases, so would the complexity and importance of the cellular contextual factors.  Thus a virus might be expected to have the simplest, most tractable sequence-structure-function relationship paradigm, bacteria perhaps a bit more complicated on up the mammals and such where I would anticipate a heavier role for transmissible molecular context.  This correlates interestingly w? the apparent genome size conundrum, in that single-celled creatures such as yeast appear to have about 6K distinct gene sequences, while tremendously more complex creatures such as mammals have only perhaps twice that number, which does not seem at all like a linear relationship.  (As I hypothesized in the late nineties)  alternate transcript splicing can certainly ad some complexity to the DNA codes functional complexity, but I don’t think that anyone is yet fully satisfied with that answer.  And I wonder if it doesn’t just add more fuel to the cellular cultural context idea, in that it raises the question of just where does all the information necessary to control and effect these splice variants come from?

Factors for mutable structure-function heritability, extra-DNA heritability

Diversity of protein forms

Degree of function (1), and diversity of function (2) of this forms

Fixation of a structure-function paradigm (permanence, stability)

A purely hypothetical example: chaperones as mediators of evolutionary change.

Stress-induced chaperones could serve to take a ‘snapshot’ of proten structures to be stabilized or could even reset structures to a starting point from which they may take multiple folding paths.  So if a protein may adopt 5 different possible stabelfolded forms, and one of them is currently dominant, a chaperone might serve to reset all of that protein species to an intermediate structural starting point, from which multiple forms are made, each w/ different functional characteristics, in essence diversifying the folded species population.  Then presumably you would want a simple mechanism for conservation of the most useful/adaptive forms

How to design experiments for extra-DNA genetics?

 May 30, 2010:

environmental change –> physiological stress –> mutation of DNA –> adaptation

–> cancer or other deleterious effects

hypothesis: stressors promote mutation for adaptation, and therefore stressors promote cancer as a by-product of a natural physiological response.

So, the apparent epidemic of cancers in humans could be a new trend in humans induced by the rapid change to civilization, industrialization and all the many changes associated w/ this trend.

So what happens if you plunk down a pedal power generator on a sidewalk in a city and let people use it, and give them a reward for doing so? And why would you want to do this? Let’s take a look at some categories of users in the target market, and some facets of human nature and physiology.

First, keep in mind that the human hardware set is a legacy product that hasn’t been significantly updated since its ca. 50,000 years ago distribution. How the analogy breaks down with regard to software and firmware revisions is up for debate (I’d say software, widely revised frequently; firmware, not so much). But the upshot is that, to the best of our knowledge, we are basically an outlandish civilization mod running on a hunter-gatherer console. In the interest of brevity for the quick-witted and the uninterested, suffice to say the human prototype runs around a lot, eats hunter-gatherer food, thinks about hunter-gatherer stuff (food, family, friends, predators, competitors, weather, story/myth/news, god[s], space and time; or something like that), and has a very direct, hands-on interaction with its world, whereas the modern human has to worry a lot about getting too fat, about getting enough selenium or whatever, about worrying itself, and generally has a somewhat more abstract interaction with the cause and effect results on one’s own life (balanced any spreadsheets lately?).

Target 1 is a ‘homeless person’, a street bum, urchin…{insert your label of choice here}. It is interesting to me that the people who, for various reasons, have chosen to most overtly eschew the dominant paradigm of civilization are the least respected and most inherently illegal in their everyday existence. We know that in the United States, psychological conditions are prevalent among the homeless, ranging from relatively commonplace conditions such as depression and chemical dependence to extreme schizophrenia and other severe disorders. The condition of and prognosis for this category of citizen is not good currently, in that the structure as we know it now tend to create a downward current which is hard to escape, and the methods of subsistence in this mode, consisting largely of begging for handouts and digging through garbage, are time-consuming/labor intensive, and further damage both the individual and the image of such individuals as useless, alien, and repulsive.

Yet, it should not be neglected how much effort and ability to survive is required to maintain such an existence, and I suspect it is in many ways strongly analogous to that of the hunter-gather, although sorely lacking in key beneficial characters of the hunter-gather experience, as are we all. Thus I do not believe it is initiative that is lacking in most humans, but mechanisms for effective action. Further, one of the simplest and most effective therapies for improvement of mental health is plain old exercise. Whereas lack of physical activity can contribute to a downward spiral of malaise and depression, initiation of even the most mild exercise routine, such as a daily walk around the block, can have a compounding positive effect to aid in an upward cycle of improvement. Physical activity is a mental health bootstrap.

Enter the street-side utility generator with positive feedback and reward.

This device converts human power into something generally useful, such as electrical power. The amount of electrical power a human can generate by mechanical action is minuscule next to the scale of current consumption via the municipal power grid to which we are accustomed, but nonetheless can have significant utility when thoughtfully applied in a small-scale, all-DC system that is highly localized, such as a portable device charging station or an LED art piece. But the power generated or the artistic beautification provided is just part of the puzzle. Additional benefit to society which is difficult to quantitatively predict, comes from the physiological benefit to the user doing the power generation. Diet and exercise are the two most powerful health factors which can be readily controlled by an individual, and offering everyone who walks by the opportunity to improve their psycho-physiological health while feeling a sense of purpose and contribution in doing so could be a much more cost effective investment than existing systems for treating only the symptoms and results of high risk factor living. Further incentivization is applied to this system in two ways: by creating a game or system of feedback which provides the user with a record or score, virtual distance traveled, high speed etc… that can be tallied and compared either individually, in teams, by location or other criteria; second, by providing a direct reward for work performed, such as a short-term food voucher to be redeemed for good, wholesome food, or any number of other creative solutions such as a photograph, transmittance of a unique email, postcard, or phone call, or even coupons or vouchers for clothing or lodging. In this model it behooves the system for the device to be viewed as an aesthetic improvement to a neighborhood, to the machine’s environs. If for example the machine is a beautiful kinetic sculpture that requires human power to make it go, then every time a person gets on that machine and powers it they are seen as doing something of immediate benefit to that area of the city, that section of street, and that benefit is shared directly by local businesses. In the ideal implementation, businesses would be clamoring to have a human power generator on their block, and offering to support it directly by offering their goods or services to be dispensed from the machine as a reward for use.

Target users 2 and 3 are the tourist and local resident. The tourist or visitor is a person looking, seeing and experiencing a city from an outside perspective. They are curious and interactive, wanting to see and to do, particularly those things that are unique or special to a given locale. Therefore I envision the tourist happily willing to donate some physical effort, try something different, to feel a part of the local community for a moment and generally just have a good time. I envision a group of tourists, one or two of which pedal while the others take pictures, and then realizing they have almost pedaled their way to a free item, go a bit longer, and a bit longer, maybe even have a friendly competition, then off they go vouchers in hand to the local business where they end up doing some shopping in addition to redeeming their prize.

User 3 is the local resident. The local user is one who thinks it’s cool to have this sculpture/charger device in their area and patronizes it because a)they simply like it and possibly enjoy the activity as well, getting exercise and watching people go by, b)they directly benefit from the activity–‘dang, my cell phone died, better charge it up’; ‘dang, i’m starving, but forgot my wallet’; ‘hey, i’ll go out for a run and get a tea and send a text or tweet while I’m out but won’t have to carry my wallet or cell phone’; and c)they become invested in the gaming aspect of the system, and wish to accrue more points for their self/team/location, etc…

Given these hypotheticals and scenarios, the device itself can be broken down into a few very doable components, and it remains only to choose some particulars from existing technologies and some cost benefit analysis for implementation of a functional machine.

Optimal design specifics:

1 Human power in: pedal, row/pull, stair-step, teeter totter, hand crank, etc…

2 Power output and storage: electrical or mechanical power storage via batteries, capacitors, raising a weight, flywheel, etc…

3 Power management: electronics control of voltage, current with universal outputs to charge user devices and to power the machine’s subsystems

4 Wireless/wired connectivity: wireless preferred for simplicity; remote administration, networking and recordkeeping, possibility for communication link provided to the user

5 User interface display

6 Immediate output/aesthetics: examples: a simple streetlamp; a color-changing flywheel persistence-of-vision-based reader board; a kinetic, rotating sculpture of illuminated and counter-rotating interlocking parts that must be ‘charged’ by the user and then gradually performs its kinetics for all to see; a van-de-graff generator that makes mini blue lightning bolts of static electricity, a transponder that sends and receives a signal from passing or geosynchronous satellites, the Intl. Space Station, etc…; a camera and photo printer

7 A printer or other system to dispense tickets/vouchers, or, alternatively a paperless system such as a digital pic which is sent instantly to the vendor offering the prize

8 Microcontroller brain of the system

My interests in magnetic resonance imaging and spectroscopy of small live critters brought me to become acquainted with the Golden Orb Weaver spider.  There are numerous species of these large and beautiful spiders in the various warm, humid corners of the world, in this case it was specifically Nephila Clavipes, which is found in the American Southeast.  Folks in Texas, Florida and Louisiana know them well as ‘Banana Spiders’, presumably because they are large and yellow.  They make enormous round webs of particularly strong silk, and these webs are referred to as ‘golden’ because they contain silk fibers that are pale yellow in color.

I found out about these guys because of a lab at Arizona State University that had the same kind of high field NMR spectrometer I was using for MRI, which they were using to investigate the structural properties of spider silk.  Further they were interested in the process of imaging the spider itself while ‘silking’ (making and secreting silk strands), but lacked the MRI probe for their spectrometer (mine being the only one in existence).

http://ednieuw.home.xs4all.nl/Spiders/Info/webthread.html

I went to visit their lab and had a great time playing with the large and beautiful spiders, who are not harmed by the process of collecting silk.  They are anesthetized briefly and gently restrained in an inverted position (on their back).  As they are handled a double fiber of silk trails behind them, and this silk line can be attached to a spool.  As the spider wakes up, this spool can be turned and the result is a circular loop of many-layered silk.  Snipping it in one spot gives you a strong white fiber resembling dental floss which can be easily handled, and in doing so you will quickly observe that it is strong stuff, and I would say, very aesthetically pleasing as well.

Infovisual.com
Under the microscope, the spider can be seen to have 8 different silk glands (as I recall), and part of the study of the silk is in determining the different material properties and structures of the multiplicity of silk the spider produces.  A great difficulty in understanding the process of silk production is that the glands are long, tapering structures apparently correlating with a progressive chemical process that starts with a liquid ‘dope’ at one end and POOF! produces an exceptionally strong and specific type of solid proteinaceous fiber at the other end.  When you dissect out one of these glands, you destroy the delicate chemical process you wish to study.  Thus the impetus to image the glands live, in an intact spider while silk is being collected, and, ideally, perform in vivo spectroscopy on the gland during the process.

I was very much in favor of this elegant application of my MRI microscope.  Unfortunately, by the time we got the whole thing set up, including shipping the equipment to Arizona and flying myself and the SMRL facilities manager out as well and staying the night in a hotel next to campus, the probe broke.  In fact within an hour of starting our work in the morning, the Y-axis gradient went dead (open circuit).  Knowing what I know now (the Y-axis gradient connection had been cobbled together in a most ugly fashion by my probe-building contractor) I would have just torn down the probe and fixed it on the spot.  At the time though we decided to scrap the whole mission, fly home, and send the probe back to the company that constructed it for me.  What a shame!

On a bio-geek tangent, however, it did get me thinking about that golden silk.  Why and how does this golden silk happen?  This beautiful and seductive spider lured me in.  It led me to cool hypothesis which I will paste below from my notes:

orb weaver golden silk hypothesis:
In examining the orb weaver, it appeared to me that the yellow markings on the abdomen are translucent patches of cuticle, with yellowish internal organs visible underneath.  My suspicion is that sunlight, shining through these patches, elicits a photochemical synthetic pathway to form the golden pigment of the characteristic yellow-tinted silk these spiders produce.  My first hypothesis regarding the golden web material was that its value to the spider is as a visual camouflage.  I am told that the spiders kept in the lab produce little or no golden silk, showing that some factor is missing in the lab environment, such as a food source.  Not all the spiders silks are tinted, nor are the tinted ones always tinted.  I suspect that the position of the translucent cuticle patches may correspond in some way to the position of the silk glands in the abdomen that make the golden silk.  The spider then sits in the center of its web for long hours in sunlight (they are native to sunny southern states such as Florida and Texas, as well as Northern Australia, Senegal, etc.), exposing these patches to sunlight for optimal photochemistry initiation.  The legs also show golden bands, and the naked cuticle areas of these bands are interspersed by black areas that are heavily bristled.  Possibly this is another way that the photochemical formation of pigment is selectively activated to effect yellow banding in the body.  Based on collected images and text found on the internet, it seems the spider’s egg sac is normally entirely golden in color, and is made in late summer to autumn, when there is a great deal of sunlight.  Potentially under this hypothesis there could be a connection between the position of translucent cuticle patches, angle of the sun, position and orientation of web design, and position and activity of the spider to maximize pigment photochemistry.  In other words, the spider may sit in the web orienting these putative solar collectors toward the angle of the sunlight in late summer to autumn.

simple expt:  expose lab spiders to broad spectrum light.

if this effects golden silk, paint over or occlude the translucent patches to see if pigment level is then affected.

if this is fruitful, obviously, there are lots of corollaries, follow up expts to determine the key light wavelength, predict and identify the pigment forming mechanisms, and so on. “

There are few things quite so elegant as a quick and decisive scientific experiment. And if it involves things of beauty, so much the better. The golden silk experiment seemed like a good one. Get some spiders, see if you can control the coloration of their silk with light.

So I ordered some spiders (found one place online to get them). They turned out to be in limited supply, and when they did come, were either dead or dying. The deal is, the retailer of terrestrial invertebrates (bugs and critters) pays someone to go out in the swamps and so forth of the Southeast and grab these hapless adult female spiders and, presumably, ship them to the retailer who is another state, who then keeps them in a greenhouse or whatever before shipping them again, to me. The spiders don’t like it much, and they are on a limited life budget to begin with. This is not some fat tarantula you can keep as a pet for many years. These critters die each year. So at their biggest and most catchable, they are already on their way out. I did however also receive one slightly golden-colored egg case. And it did in fact become a swarm of tiny spiderlings, silking like mad. Suddenly I was in the spider rearing business.
   

I built them a little structure on which to make webs, which they quickly silked up in a disorderly tangle of single silk lines, like a house being TP’d by teenagers, and then they clung together in a big mass upon it. Efforts to feed them were largely unsuccessful. I had access to a bounty of laboratory fruit flies, which were larger than the spiderlings, and it wasn’t clear that the spiderlings had much interest in capturing at eating food anyway. Within a few days their interest changed from clustering to dispersing: I took them outside in the sun on a clear day and removed the web support structure from the enclosing jar for a better look. Immediate ‘kiting’ ensued. Kiting is when a baby spider releases a long strand of silk from its abdomen, catches the wind, and takes off like an errant paraglider. I believe it was described most familiarly in Charlottes Web. It was with terror and awe that I watched one then another and another of my tiny spiderlings take flight and begin to drift away on gentle zephyrs. I didn’t want to lose them, and I didn’t want to be responsible, however unlikely, for introducing a foreign species into the Western California ecosystem, nor did I want my poor, vulnerable little charges to be lost, alone and afraid to the certain doom of a habitat that has no place for them. I was after all trying to raise test subjects for future use. So I stuffed them back into the jar as quickly as possible. After that it was basically a long and tedious process of watching them outgrow one web structure/enclosure after another, eat each other, die off, escape into the rafters of my basement, and generally fail to flourish in culture, as I struggled to keep up with their needs for space, food, warmth, and humidity, without great success. They never made it to my test enclosures fitted with different spectra of lights.

At the end of all this it was painfully clear that a likely much simpler way to do this experiment would be to go to the spiders’ habitat and simply work on them there. I think they proliferate into their full golden glory some time in the spring to early summer in places like the everglades, and in fact much of the American Southeast, not to mention many other parts of the world (Asia, Australia, Africa) so perhaps one of these days the variables will align for me to be in the right place at the right time to glue little blinders on golden spiders and see if I can whiten their webs, or not.

Bibliography:
Got Silk. – New York Times
Spider silks: recombinant synthesis, assembly, spinning, and engineering of synthetic proteins by Thomas Scheibel*
Amyloidogenic nature of spider silk by John M. Kenney, David Knight, Michael J. Wise and Fritz Vollrath
Lab Methods for Maintaining Spiders
Mechanical Differences of Major Ampullate Silk Fibers from Nephila clavipes and Argiope aurantia
MIT lab works to mimic spider silk – MIT News Office
Nephila Anatomy
Nutritional requirements for web synthesis in the tetragnathid spider Nephila clavipes
Solvent Removal during Synthetic and Nephila Fiber Spinning
Use of spider silk fibres as an innovative material in a biocompatible artificial nerve conduit
VARIATION IN THE CHEMICAL COMPOSITION OF ORB WEBS BUILT BY THE SPIDER NEPHILA CLAVIPES

Purpose: Goat-aided travel with a set of communication and subsistence tools, for an indefinite period of time

Goal: Possibly to walk across the US (the world?) with goats. To be able to live outdoors and be nomadic, yet still be a modern, informed person with connectivity to the world

Why do I want to do this??

Let’s say you want to get away, really get away, whatever that means. The point is, what constitutes a minimal autonomous living unit? And what can possibly be cooler than camping with goats? Somehow this vision grabs me on some very vital level. It’s not so much that I want to leave everything, or escape or whatever, so much as I want to see more. I want to know what happens if a modern, born-into-civilization human (me) lives closer to nature. I want to see if I can continue to be connected to the world of people and global communication, at the same time I can be almost anywhere at all. Can I wake up on the edge of a pine forest instead of a developed urban area, swim in a creek or hot spring instead of taking a shower, and then go about my work day? If one can telecommute from home, why not a jaggedy rock outcropping in the Sonora Desert, or the Rockies, or anywhere? Is it possible to walk, and just keep walking, go anywhere, not limited by roads or even trails, and keep right on being connected to the world? For the first time there are tiny devices that can do video conferencing, internet, voice, and computing. So I’m imagining the set of tools and provisions it would take to go nomadic, with goats, indefinitely. How much power (electric) is needed versus what can be generated? How much weight? How much food, water, clothing, shelter? The goats can do it and require almost no provisions in most places most of the time.

Firstly, camping with goats is great. They have quirky, interesting, mischievous personalities, and they or naturally social animals that prefer to live in a tight-knit herd that travels together. They have natural roles within the herd such as leader, lookout, and even the job of making sure everyone stays together. They see well in the dark and remember trails and paths taken in the past extremely well. They sleep in a group, fitfully, so that there is always someone keeping lookout through the night. If you let them, they are happy to curl up next to you and share all the extra heat they seem to have. They are expert foragers, finding food just about anywhere, and can go without water much better than a person can. They are much better at carrying packs than people are and do so much more happily. They can go places far beyond that of any other pack animal and most humans. Their environmental impact as transient pack animals tends to be extremely low and in many cases is actually beneficial for invasive and noxious weed removal and browsing of trees that nowadays lack the formerly large population of grazing animals that existed in many ecosystems previously.

Camping with a backpack is kind of okay, but also kind of lousy. Especially if you are going long term and committed to bringing various gear, as I am proposing here. You plod along, encumbered, in pain, putting massive wear on your body. You relish the moments of stopping and slipping out of that pack. You look at things along the trail and think you might go over and investigate if it weren’t for this huge heavy pack. Any misstep is more dangerous and harder to steady with all the extra weight up high on your body. The goats, on the other hand, seem to take to packing naturally. I have never seen them shy away from putting on the pack, and believe me, goats are not shy about sharing their opinions on what they want or don’t want. Most of the time they just seem excited to be part of the herd going on an expedition, packs or not. They are, after all, domesticated animals that have traveled in herds with humans for a long, long, long time. Bike camping is good too, but besides the similar considerations as those for backpacking, it means more gear to maintain the bike, and of course fundamental limitation on where you can go. For most people, this means traveling on the same roads as cars and sharing the skinny little shoulder, when there is one, with the potentially lethal cars racing by, providing noxious exhaust for you to breathe…not that that’s necessarily a bad way to spend your time, but my point in this imaginable is to get away from that whole situation.

Considerations: All gear must be weighed and size/mass distribution among goats considered minimal gear and functionality desires must be determined route/climate capability is a major component, as is weather As in other kinds of packing, the goal is to MINIMIZE!

WHAT TO PACK:

SOME QUESTIONS:

REFERENCES:

Books:   Goat Packing by John Mionczynski             Sites:   Wikipedia Pack Goat